RRC ID 32672
Author Shirasawa K, Hirakawa H, Nunome T, Tabata S, Isobe S.
Title Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato.
Journal Plant Biotechnol. J.
Abstract Genome-wide mutations induced by ethyl methanesulfonate (EMS) and gamma irradiation in the tomato Micro-Tom genome were identified by a whole-genome shotgun sequencing analysis to estimate the spectrum and distribution of whole-genome DNA mutations and the frequency of deleterious mutations. A total of ~370 Gb of paired-end reads for four EMS-induced mutants and three gamma-ray-irradiated lines as well as a wild-type line were obtained by next-generation sequencing technology. Using bioinformatics analyses, we identified 5920 induced single nucleotide variations and insertion/deletion (indel) mutations. The predominant mutations in the EMS mutants were C/G to T/A transitions, while in the gamma-ray mutants, C/G to T/A transitions, A/T to T/A transversions, A/T to G/C transitions and deletion mutations were equally common. Biases in the base composition flanking mutations differed between the mutagenesis types. Regarding the effects of the mutations on gene function, >90% of the mutations were located in intergenic regions, and only 0.2% were deleterious. In addition, we detected 1,140,687 spontaneous single nucleotide polymorphisms and indel polymorphisms in wild-type Micro-Tom lines. We also found copy number variation, deletions and insertions of chromosomal segments in both the mutant and wild-type lines. The results provide helpful information not only for mutation research, but also for mutant screening methodology with reverse-genetic approaches.
Volume 14(1)
Pages 51-60
Published 2016-1
DOI 10.1111/pbi.12348
PMID 25689669
PMC PMC5023996
MeSH Base Sequence DNA Copy Number Variations / genetics Ethyl Methanesulfonate Gamma Rays* Genes, Plant Genome, Plant* INDEL Mutation / genetics Lycopersicon esculentum / genetics* Lycopersicon esculentum / radiation effects* Mutation / genetics* Plants, Genetically Modified Polymorphism, Single Nucleotide / genetics Sequence Analysis, DNA Surveys and Questionnaires*
IF 7.443
Times Cited 15
WOS Category PLANT SCIENCES BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Resource
Tomato TOMJPG1269-1 TOMJPG1679-1 TOMJPG2893-1 TOMJPE6018-1 EMS bulk set C TOMJPF00001